1-182570983-C-T

Variant names:

• chr1-182570983-C-T
• rs12729828

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.11 in 152,142 control chromosomes in the GnomAD database, including 990 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16698 AN: 152024 Hom.: 990 Cov.: 32

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.102

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.110 AC: 16705 AN: 152142 Hom.: 990 Cov.: 32 AF XY: 0.108 AC XY: 8048 AN XY: 74376

African (AFR) AF: 0.0987 AC: 4097 AN: 41506

American (AMR) AF: 0.0871 AC: 1332 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5192

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4822

European-Finnish (FIN) AF: 0.138 AC: 1451 AN: 10548

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9102 AN: 68004

Other (OTH) AF: 0.101 AC: 214 AN: 2110

Alfa AF: 0.123 Hom.: 156

Bravo AF: 0.107

Asia WGS AF: 0.0180 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12729828; hg19: chr1-182540118;